The Psycho Pirate still has Green Lantern under his spell and later enchants the Flash as the rest of the JSA try to stop him at his Earth-1 hidden headquarters. He is defeated by Wildcat's punch, who is unaffected by his fear gaze. Meanwhile, Bruce Wayne plans to arrest the JSA as he calls in for some heavy backup while the JSAers are still on Earth-1 in the JLA satellite.

The JSA is divided against itself with one group -- consisting of Hawkman, Green Lantern, Flash, Star Spangled Kid, Wildcat, Dr. Fate -- facing off against a group with Commissioner Bruce Wayne behind them -- Robin, Wonder Woman, Starman, Dr. Mid-Nite, Hourman -- seeking to arrest the others on trumped up charges. Though Power Girl is hurt, Superman and Dr. Fate save the day when Superman stops the fight and Fate reveals that Commissioner Wayne is being controlled by the Psycho Pirate.

As the briefly reunited JSAers go their separate ways, Huntress and Wildcat are left alone at headquarters, as she learns that he knows her true identity. They are interrupted when Star Spangled Kid sends out a distress call as he's fighting a new foe, Strike Force, and no one else has answered the call due to personal reasons.

The newly added member Huntress and Wildcat go off to save Star-Spangled Kid from the Strike Force, who unbeknownst to the Kid is being run by his evil nephew, who has taken control of the Pemberton fortune and is using it for evil means. The three heroes defeat Strike Force, but the Kid leaves the team, citing his needs to regain his lost fortune and identity once more.

The Master Summoner, asleep for more than a millennium awakens to challenge the JSA, with them not knowing of the consequences of accepting the challenge. Dr. Fate finds out that as they continue to fight, he gets stronger, and once powered up enough would destroy Earth-2. The JSAers then face the difficult task of doing nothing as the world goes mad so as to defeat his plan, thereby putting him away again for another millennium.

As Jensen continues his reign of terror on the top of Gotham Twin Towers, Wayne has escaped his wrath and is inside one of the towers with a Batman exhibit inside its museum. Remembering all that he did as Batman up until his wife's death, he decides he has no other choice but to put on the costume one last time and face Jensen. The resulting battle kills them both and reveals Wayne as Gotham's longtime guardian.

The JSA faces off against Fredrick Vaux, the true mastermind behind Jensen acquiring his mystic powers. Vaux, who had made a pact with a demon to destroy Earth-2's heroes and their legacies, is defeated by the power of the JSA and Fate's magic, along with Bruce's heroic spirit. A side effect of this victory was that Fate was able to have the world remember Bruce Wayne and Batman as two separate people, thereby keeping his double identity a secret, as well as Robin's and Huntress's.

The JSA must find a deadly capsule containing a poisonous substance that could kill millions if released. The capsule is eventually recovered from a stray dog just as it's about to release its toxins and contained by Dr. Fate.

As the JSAers go their separate ways after Mr. Terrific's funeral, Power Girl wonders why the team disbanded in 1951 and Huntress relates the story as she heard it. After a case involving their being kidnapped by a man with foreign interests, the JSA was summoned before Congress and their loyalty to their country questioned. Rather than reveal their identities, the heroes disappeared and retired.